pl-fs6-recon-all

Abstract

ChRIS plugin to run the FreeSurfer 6.0 recon-all stream.

Building the container

docker build -t pwighton/pl-fs6-recon-all .

Running

Assign an "input" directory to /subjects and an output directory to /outgoing

Also required is the environment variable FS_KEY that is a base64 encoding of the FreeSurfer license file. You can apply for a license file here. Once you have the file, run the following command to generate the FS_KEY string

base64 -w999 ~/Downloads/license.txt

The current string for the ChRIS license file is: cnVkb2xwaC5ubXJAZ21haWwuY29tCjM1Mzc3CiAqQ0liU0R6Z01RQlFRCiBGU0JBUC84aHBWOU0yCg==. Inside of chris, this is set by default

Examples

This will run the entire stream (several hours):

docker run -it --rm \
  -v /tmp/sub/in/:/subjects \
  -v /tmp/sub/out:/outgoing \
  pwighton/pl-fs6-recon-all \
    fs6_recon_all.py \
      --subject bert 
      /incomming /outgoing

This will only do skull stripping. See here for more info on the stream

	docker run -it --rm \
	  -v /tmp/sub/in/:/subjects \
	  -v /tmp/sub/out:/outgoing \
	  pwighton/pl-fs6-recon-all \
		fs6_recon_all.py \
		  --subject bert \
		  --ar1 \
		  /incomming /outgoing

To convert an .mgz outputs to .nii.gz

docker run -it --rm \
  -e FS_KEY='cnVkb2xwaC5ubXJAZ21haWwuY29tCjM1Mzc3CiAqQ0liU0R6Z01RQlFRCiBGU0JBUC84aHBWOU0yCg==' \
  -v /tmp/sub/out:/tmp/sub/out \
  corticometrics/fs6-base \
    mri_convert /tmp/sub/out/subjects/bert/mri/brainmask.mgz \
                /tmp/sub/out/subjects/bert/mri/brainmask.nii.gz

This will convert brainmask.mgz to brainmask.nii.gz